Zinc in PDB 5ls6: Structure of Human Polycomb Repressive Complex 2 (PRC2) with Inhibitor

All present enzymatic activity of Structure of Human Polycomb Repressive Complex 2 (PRC2) with Inhibitor:
2.1.1.43;

The structure of Structure of Human Polycomb Repressive Complex 2 (PRC2) with Inhibitor, PDB code: 5ls6 was solved by Y.Zhang, N.Justin, S.Chen, J.Wilson, S.Gamblin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	68.84 / 3.47
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	131.310, 170.270, 275.540, 90.00, 90.00, 90.00
R / Rfree (%)	22.9 / 29.9

The structure of Structure of Human Polycomb Repressive Complex 2 (PRC2) with Inhibitor also contains other interesting chemical elements:

Fluorine

(F)

8 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 32;

Binding sites:

The binding sites of Zinc atom in the Structure of Human Polycomb Repressive Complex 2 (PRC2) with Inhibitor (pdb code 5ls6). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 32 binding sites of Zinc where determined in the Structure of Human Polycomb Repressive Complex 2 (PRC2) with Inhibitor, PDB code: 5ls6:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 32 in the Structure of Human Polycomb Repressive Complex 2 (PRC2) with Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Human Polycomb Repressive Complex 2 (PRC2) with Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn801 b:70.6 occ:1.00 SG A:CYS289 1.8 67.8 0.9 ND1 A:HIS297 2.2 73.1 1.0 SG A:CYS286 2.3 83.1 1.0 SG A:CYS294 2.5 70.3 0.9 CB A:CYS294 2.9 77.2 1.0 CE1 A:HIS297 2.9 75.1 1.0 CG A:HIS297 3.3 74.6 1.0 CB A:CYS286 3.3 84.9 1.0 CB A:CYS289 3.4 70.4 1.0 CB A:HIS297 3.7 74.2 1.0 N A:CYS289 3.9 70.7 1.0 NE2 A:HIS297 4.1 78.0 1.0 N A:HIS297 4.1 73.0 1.0 CA A:CYS289 4.2 72.0 1.0 CD2 A:HIS297 4.3 78.4 1.0 CA A:CYS294 4.5 80.7 1.0 CB A:LEU296 4.6 70.7 1.0 CA A:HIS297 4.6 72.9 1.0 CA A:CYS286 4.8 82.6 1.0 CB A:ARG288 4.9 68.2 1.0 C A:CYS289 4.9 72.6 1.0 O A:HIS297 5.0 74.5 1.0

Zinc binding site 2 out of 32 in the Structure of Human Polycomb Repressive Complex 2 (PRC2) with Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Human Polycomb Repressive Complex 2 (PRC2) with Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn802 b:0.9 occ:1.00 SG A:CYS463 1.9 78.7 1.0 SG A:CYS452 2.4 0.8 0.9 SG A:CYS320 2.8 95.7 1.0 CB A:CYS320 2.9 0.4 1.0 SG A:CYS324 3.0 0.4 1.0 CB A:CYS463 3.1 82.4 1.0 CB A:CYS452 3.4 0.7 1.0 CA A:CYS452 3.5 0.0 1.0 CA A:CYS320 3.5 0.4 1.0 N A:CYS452 3.8 98.1 1.0 CD1 A:TYR325 3.9 0.1 1.0 CB A:CYS324 4.1 0.0 1.0 N A:CYS320 4.1 0.3 1.0 CA A:CYS324 4.2 0.4 1.0 N A:TYR325 4.2 0.3 1.0 CE1 A:TYR325 4.3 0.8 1.0 CA A:CYS463 4.4 88.6 1.0 C A:PHE451 4.5 92.7 1.0 C A:CYS324 4.7 0.5 1.0 C A:CYS320 4.8 0.6 1.0 O A:PHE451 4.8 84.0 1.0 C A:CYS452 4.9 0.2 1.0

Zinc binding site 3 out of 32 in the Structure of Human Polycomb Repressive Complex 2 (PRC2) with Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Human Polycomb Repressive Complex 2 (PRC2) with Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn803 b:65.1 occ:1.00 SG A:CYS530 1.9 74.0 1.0 SG A:CYS549 2.3 79.0 1.0 SG A:CYS543 2.5 62.4 1.0 SG A:CYS553 2.6 71.2 1.0 CB A:CYS530 3.1 78.5 1.0 CB A:CYS553 3.2 78.1 1.0 CB A:CYS549 3.2 81.0 1.0 CB A:CYS543 3.3 61.1 1.0 ZN A:ZN804 3.6 56.3 1.0 ZN A:ZN805 4.1 66.8 1.0 SG A:CYS523 4.4 81.5 1.0 CA A:CYS530 4.5 74.2 1.0 CG A:ARG556 4.5 67.9 1.0 CB A:ASN555 4.6 71.5 1.0 CA A:CYS553 4.7 80.7 1.0 CA A:CYS549 4.7 78.9 1.0 NE A:ARG556 4.7 69.4 1.0 CA A:CYS543 4.7 59.5 1.0 N A:CYS530 4.8 69.2 1.0 CB A:CYS547 4.9 55.2 1.0

Zinc binding site 4 out of 32 in the Structure of Human Polycomb Repressive Complex 2 (PRC2) with Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Human Polycomb Repressive Complex 2 (PRC2) with Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn804 b:56.3 occ:1.00 SG A:CYS523 2.2 81.5 1.0 SG A:CYS534 2.4 65.9 1.0 NE2 A:HIS525 2.4 82.0 1.0 SG A:CYS530 2.5 74.0 1.0 CE1 A:HIS525 2.6 82.3 1.0 CB A:CYS530 3.4 78.5 1.0 CB A:CYS523 3.4 76.1 1.0 CD2 A:HIS525 3.5 83.8 1.0 ZN A:ZN803 3.6 65.1 1.0 ZN A:ZN805 3.7 66.8 1.0 ND1 A:HIS525 3.7 83.3 1.0 SG A:CYS543 3.8 62.4 1.0 CB A:CYS534 3.8 73.5 1.0 CA A:CYS530 3.8 74.2 1.0 CB A:CYS549 4.2 81.0 1.0 CG A:HIS525 4.2 81.9 1.0 N A:CYS530 4.5 69.2 1.0 SG A:CYS549 4.6 79.0 1.0 CA A:CYS523 4.7 75.8 1.0 C A:CYS523 4.7 76.2 1.0 N A:ASP524 4.9 83.9 1.0 SG A:CYS536 4.9 58.7 0.9 CA A:CYS534 4.9 72.5 1.0 O A:CYS523 5.0 70.9 1.0

Zinc binding site 5 out of 32 in the Structure of Human Polycomb Repressive Complex 2 (PRC2) with Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of Human Polycomb Repressive Complex 2 (PRC2) with Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn805 b:66.8 occ:1.00 SG A:CYS547 2.2 50.8 1.0 SG A:CYS543 2.3 62.4 1.0 SG A:CYS523 2.3 81.5 1.0 SG A:CYS536 2.4 58.7 0.9 CB A:CYS543 3.1 61.1 1.0 CB A:CYS536 3.3 62.6 1.0 CA A:CYS543 3.3 59.5 1.0 CB A:CYS523 3.4 76.1 1.0 CB A:CYS547 3.5 55.2 1.0 ZN A:ZN804 3.7 56.3 1.0 N A:CYS523 3.9 78.5 1.0 ZN A:ZN803 4.1 65.1 1.0 N A:CYS543 4.2 61.1 1.0 SG A:CYS534 4.2 65.9 1.0 CA A:CYS523 4.2 75.8 1.0 C A:CYS543 4.5 57.5 1.0 N A:GLU544 4.7 61.6 1.0 CA A:CYS536 4.7 66.8 1.0 SG A:CYS530 4.7 74.0 1.0 O A:PHE542 4.7 64.8 1.0 O A:CYS523 4.7 70.9 1.0 CA A:CYS547 4.8 56.3 1.0 C A:CYS523 4.8 76.2 1.0 CE1 A:TYR520 4.9 67.2 1.0 C A:PHE542 4.9 61.6 1.0 SG A:CYS549 4.9 79.0 1.0 N A:CYS536 4.9 65.5 1.0 C A:PRO522 5.0 75.2 1.0

Zinc binding site 6 out of 32 in the Structure of Human Polycomb Repressive Complex 2 (PRC2) with Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of Human Polycomb Repressive Complex 2 (PRC2) with Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn806 b:53.4 occ:1.00 SG A:CYS588 2.1 71.6 1.0 SG A:CYS566 2.4 71.3 1.0 SG A:CYS580 2.4 52.7 1.0 SG A:CYS601 2.8 80.2 1.0 CB A:CYS588 2.9 74.7 1.0 CB A:CYS601 3.5 86.9 1.0 ZN A:ZN808 3.5 55.3 1.0 SG A:CYS560 3.5 65.3 1.0 CB A:CYS580 3.7 50.4 1.0 CB A:CYS566 3.9 75.5 1.0 ZN A:ZN807 4.0 55.0 1.0 CB A:ALA590 4.3 73.7 1.0 CA A:CYS588 4.4 76.4 1.0 CA A:CYS601 4.5 85.4 1.0 CB A:CYS585 4.6 60.7 1.0 N A:ALA590 4.7 68.5 1.0 O A:ALA564 4.8 89.7 1.0 O A:GLN565 4.9 94.3 1.0 C A:CYS588 4.9 74.2 1.0 CB A:ASN603 4.9 81.1 1.0 SG A:CYS585 5.0 58.0 1.0

Zinc binding site 7 out of 32 in the Structure of Human Polycomb Repressive Complex 2 (PRC2) with Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of Human Polycomb Repressive Complex 2 (PRC2) with Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn807 b:55.0 occ:1.00 SG A:CYS585 2.1 58.0 1.0 SG A:CYS573 2.2 72.5 1.0 SG A:CYS560 2.5 65.3 1.0 SG A:CYS580 2.8 52.7 1.0 CB A:CYS560 2.9 66.1 1.0 CB A:CYS573 3.3 73.3 1.0 CB A:CYS585 3.3 60.7 1.0 N A:CYS560 3.4 65.2 1.0 CB A:CYS580 3.4 50.4 1.0 CA A:CYS580 3.7 53.6 1.0 CA A:CYS560 3.7 67.4 1.0 ZN A:ZN808 3.7 55.3 1.0 ZN A:ZN806 4.0 53.4 1.0 SG A:CYS571 4.1 55.8 1.0 C A:GLY559 4.4 62.0 1.0 CA A:CYS585 4.5 62.5 1.0 N A:CYS580 4.5 55.1 1.0 CA A:CYS573 4.5 74.7 1.0 N A:ASP581 4.6 56.8 1.0 C A:CYS560 4.6 69.2 1.0 O A:CYS560 4.6 67.6 1.0 SG A:CYS588 4.7 71.6 1.0 C A:CYS580 4.7 55.6 1.0 N A:CYS573 4.7 67.2 1.0 CA A:GLY559 4.9 62.2 1.0 SG A:CYS566 4.9 71.3 1.0

Zinc binding site 8 out of 32 in the Structure of Human Polycomb Repressive Complex 2 (PRC2) with Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of Human Polycomb Repressive Complex 2 (PRC2) with Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn808 b:55.3 occ:1.00 SG A:CYS560 2.3 65.3 1.0 SG A:CYS571 2.3 55.8 1.0 SG A:CYS562 2.5 56.6 1.0 CB A:CYS566 2.7 75.5 1.0 SG A:CYS566 2.9 71.3 1.0 CB A:CYS560 2.9 66.1 1.0 CB A:CYS562 3.1 66.8 1.0 CB A:CYS571 3.3 59.8 1.0 ZN A:ZN806 3.5 53.4 1.0 ZN A:ZN807 3.7 55.0 1.0 CA A:CYS566 4.2 80.2 1.0 SG A:CYS580 4.2 52.7 1.0 CA A:CYS571 4.3 61.5 1.0 CA A:CYS560 4.4 67.4 1.0 N A:CYS562 4.4 75.8 1.0 CA A:CYS562 4.4 71.2 1.0 CB A:CYS588 4.5 74.7 1.0 SG A:CYS588 4.6 71.6 1.0 C A:CYS560 4.8 69.2 1.0 O A:ALA564 4.8 89.7 1.0 CD A:PRO572 4.9 72.3 1.0 SG A:CYS573 4.9 72.5 1.0 CB A:CYS573 4.9 73.3 1.0 O A:CYS566 5.0 72.0 1.0

Zinc binding site 9 out of 32 in the Structure of Human Polycomb Repressive Complex 2 (PRC2) with Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Structure of Human Polycomb Repressive Complex 2 (PRC2) with Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn801 b:68.5 occ:1.00 SG D:CYS294 2.1 69.2 0.9 ND1 D:HIS297 2.1 59.5 1.0 SG D:CYS289 2.1 62.6 0.9 SG D:CYS286 2.3 75.0 1.0 CE1 D:HIS297 2.9 61.4 1.0 CB D:CYS294 3.1 68.5 1.0 CG D:HIS297 3.2 62.6 1.0 CB D:CYS286 3.2 71.2 1.0 CB D:CYS289 3.6 65.0 1.0 CB D:HIS297 3.7 64.9 1.0 N D:CYS289 3.9 66.8 1.0 NE2 D:HIS297 4.0 62.6 1.0 N D:HIS297 4.2 71.0 1.0 CD2 D:HIS297 4.2 62.9 1.0 CA D:CYS289 4.3 68.0 1.0 CA D:CYS294 4.6 69.7 1.0 CA D:HIS297 4.6 68.0 1.0 CB D:ARG288 4.6 63.4 1.0 CA D:CYS286 4.7 70.5 1.0 CB D:LEU296 4.7 64.0 1.0 C D:ARG288 4.7 65.1 1.0 C D:CYS289 5.0 69.8 1.0 O D:CYS286 5.0 70.9 1.0 N D:ARG288 5.0 64.7 1.0 N D:LEU296 5.0 64.2 1.0 CA D:ARG288 5.0 64.2 1.0

Zinc binding site 10 out of 32 in the Structure of Human Polycomb Repressive Complex 2 (PRC2) with Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Structure of Human Polycomb Repressive Complex 2 (PRC2) with Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn802 b:84.5 occ:1.00 SG D:CYS320 2.1 97.8 1.0 SG D:CYS452 2.1 80.1 0.9 SG D:CYS463 2.5 67.1 1.0 CB D:CYS320 2.7 0.6 1.0 SG D:CYS324 3.0 0.0 1.0 CB D:CYS452 3.1 79.5 1.0 CB D:CYS463 3.1 66.4 1.0 CA D:CYS320 3.4 0.3 1.0 CA D:CYS452 3.4 76.8 1.0 N D:CYS320 3.9 0.8 1.0 N D:CYS452 3.9 76.5 1.0 CB D:CYS324 4.0 0.2 1.0 CD1 D:TYR325 4.1 89.8 1.0 CA D:CYS324 4.2 0.3 1.0 N D:TYR325 4.4 94.6 1.0 CA D:CYS463 4.5 71.7 1.0 CE1 D:TYR325 4.6 88.6 1.0 C D:PRO319 4.7 0.2 1.0 C D:CYS452 4.7 72.5 1.0 C D:CYS320 4.8 0.3 1.0 C D:CYS324 4.9 97.8 1.0 C D:PHE451 4.9 76.4 1.0

R.G.Vaswani, V.S.Gehling, L.A.Dakin, A.S.Cook, C.G.Nasveschuk, M.Duplessis, P.Iyer, S.Balasubramanian, F.Zhao, A.C.Good, R.Campbell, C.Lee, N.Cantone, R.T.Cummings, E.Normant, S.F.Bellon, B.K.Albrecht, J.C.Harmange, P.Trojer, J.E.Audia, Y.Zhang, N.Justin, S.Chen, J.R.Wilson, S.J.Gamblin. Identification of (R)-N-((4-Methoxy-6-Methyl-2-Oxo-1,2-Dihydropyridin-3-Yl) Methyl)-2-Methyl-1-(1-(1-(2,2,2-Trifluoroethyl) Piperidin-4-Yl)Ethyl)-1H-Indole-3-Carboxamide (Cpi-1205), A Potent and Selective Inhibitor of Histone Methyltransferase EZH2, Suitable For Phase I Clinical Trials For B-Cell Lymphomas. J. Med. Chem. V. 59 9928 2016.
ISSN: ISSN 1520-4804
PubMed: 27739677
DOI: 10.1021/ACS.JMEDCHEM.6B01315